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Genes Fold Enrichment Color Codes
  • Gene Name, Canonical Transcript - gene identifiers from gnomAD database (Build 37)
  • GeVIR % - gene rank measured in percentiles based on Gene Variation Intolerance Ranking (GeVIR) (low values indicate more variation intolerant genes, which is also true for "LOEUF %" and "VIRLoF %"). GeVIR is a method which we developed and applied on a list of 19,361 genes to sort them based on number, length and evolutionary conservation of regions without functional variants (i.e. between two missense, loss-of-function, insertion or delition variants) in gnomAD database (version 2.0.1). Only canonical transcripts were analysed.
  • LOEUF % - gene rank measured in percentiles based gnomAD loss-of-function observed/expected upper bound fraction (LOEUF) (see Figure 1). For more information about this metric, please read "Constraint" section of MacArthur Lab blog post. If you use this metric please cite gnomAD flagship paper and use most up-to-date values from gnomAD website.

    LoF observed/expected (o/e) upper Confidence Interval (CI)

    Figure 1. Screenshot of ELN gene constraint metrics from gnomAD browser

  • VIRLoF % - gene rank measured in percentiles based on both GeVIR and gnomAD LOEUF (shows the best overall performance, see Figure 2). If you use this metric please cite both GeVIR and gnomAD flagship paper.
  • GeVIR AD, LOEUF AD, VIRLoF AD, GeVIR AR, LOEUF AR, VIRLoF AR - to help users interpret gene ranks, we calculated fold enrichment of Autosomal Dominant (AD) and Autosomal Recessive (AR) genes with known molecular basis of disorder in OMIM in a range of +-5% of gene X (see Figure 2). Statistical significant fold enrichements (Fisher Exact Test p-value < 1e-5) are shown in bold in the table. For example CDK19 gene's GeVIR % is 2.37, so examined range is from 0 (2.37-5, rounded to minimal percentile) to 7.37% (2.37+5). Genes in this range are ~4 times more often (4.05 fold enrichement) associated with AD diseases and ~4 times less often (0.25 fold enrichement) associated with AR diseases. Both enrichment of AD genes and deficiency of AR genes is statistical significant. Thus GeVIR metric adds supportive evidence that CDK19 is more likely to be associated with AD than AR disease.

    Gene Percentiles AD AR Fold Enrichment

    Figure 2. Fold Enrichment of known Autosomal Dominant (AD) and Autosomal Recessive (AR) genes of each gene in the ranked lists (GeVIR, LOEUF, VIRLoF. AD genes are enriched among top ranked genes (lowest percentiles), whereas AR genes are enriched among middle ranked genes (approximetly 35-65 percentiles). Combined metric (VIRLoF, purple) shows the best perfornance, i.e. high ranked genes are more often associated with AD than AR diseases, low ranked genes are less often associated with both AD and AR diseases.
Gene Name Canonical Transcript GeVIR % LOEUF % VIRLoF % GeVIR AD LOEUF AD VIRLoF AD GeVIR AR LOEUF AR VIRLoF AR
MRAS ENST00000289104 0.52 16.48 5.75 4.38 1.80 3.30 0.19 0.69 0.28
PSMA6 ENST00000261479 0.53 7.42 1.83 4.40 2.54 4.21 0.19 0.39 0.24
BTBD10 ENST00000278174 0.53 32.68 14.32 4.39 0.85 2.00 0.19 1.45 0.60
KPNB1 ENST00000290158 0.54 0.90 0.08 4.39 4.08 4.86 0.19 0.29 0.15
EBF3 ENST00000368648 0.54 2.99 0.50 4.39 3.47 4.72 0.19 0.28 0.17
KIF2A ENST00000407818 0.55 3.65 0.63 4.38 3.35 4.65 0.19 0.31 0.19
HNRNPA0 ENST00000314940 0.55 17.33 6.20 4.38 1.61 3.16 0.19 0.75 0.32
CLTC ENST00000269122 0.56 0.80 0.07 4.40 4.11 4.85 0.19 0.27 0.15
PIK3CA ENST00000263967 0.56 1.81 0.23 4.39 3.79 4.84 0.19 0.26 0.18
KCNJ3 ENST00000295101 0.57 3.93 0.74 4.39 3.29 4.58 0.19 0.31 0.20
ST7 ENST00000265437 0.57 9.70 2.63 4.38 2.45 4.02 0.19 0.50 0.23
VAMP2 ENST00000316509 0.58 20.34 7.81 4.38 1.44 2.62 0.19 0.74 0.34
HSD17B10 ENST00000168216 0.58 19.28 7.28 4.38 1.47 2.80 0.19 0.76 0.34
KRAS ENST00000256078 0.59 67.03 32.02 4.37 0.54 0.90 0.19 1.24 1.59
DHX9 ENST00000367549 0.59 1.30 0.13 4.37 3.98 4.86 0.19 0.27 0.18
CHD4 ENST00000357008 0.60 2.74 0.43 4.36 3.53 4.75 0.19 0.29 0.17
PSMC6 ENST00000445930 0.60 8.64 2.29 4.36 2.49 4.04 0.19 0.47 0.22
SATB2 ENST00000417098 0.61 0.88 0.09 4.36 4.09 4.88 0.19 0.29 0.15
CELF2 ENST00000450189 0.61 1.43 0.15 4.35 3.94 4.84 0.19 0.27 0.18
RPS26 ENST00000356464 0.62 26.10 10.99 4.35 1.20 2.21 0.19 1.09 0.44
FBXO11 ENST00000403359 0.62 1.03 0.10 4.34 4.05 4.89 0.19 0.28 0.16
HNRNPH1 ENST00000356731 0.63 1.35 0.14 4.34 3.97 4.85 0.19 0.27 0.18
STAT1 ENST00000361099 0.64 4.73 0.96 4.34 3.28 4.46 0.19 0.31 0.21
HDAC2 ENST00000519065 0.64 1.21 0.12 4.35 4.02 4.87 0.19 0.27 0.18
NR2F1 ENST00000327111 0.65 5.85 1.29 4.35 2.85 4.37 0.19 0.35 0.21

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